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There is a metro tunnel at grayditch, look for a scientist and you have the opratunity to kill the queen, or help him and you will get a injection that reduces damsge to fire that. In the meen time you just have to kill those buggers.

I tried to do this mission at a very low level on my first playthrough. I didn't even have a gun and had to beat each of the giant ants with a baseball bat. If you need weapons, its pretty easy to clear out the raiders in the Satcom Array NN-03D (it's at the top of the map almost directly north or Magaton). (Even at a low level) once you've an assut rifle and a fair bit of ammo this will be easy.